public void MergeDbSnp1KpEvsRefMinor()
{
const string vcfLine1 = "1 69428 rs140739101 T G . . RS=140739101;RSPOS=69428;dbSNPBuildID=134;SSR=0;SAO=0;VP=0x050200000a05140026000100;WGT=1;VC=SNV;S3D;NSM;REF;ASP;VLD;KGPhase3;CAF=0.981,0.01897;COMMON=1";
//vcf line is modified
const string vcfLine2 = "1 69428 rs140739101 T G 100 PASS AC=4956;AF=0.989617;AN=5008;NS=2504;DP=17611;EAS_AF=0.003;AMR_AF=0.036;AFR_AF=0.0015;EUR_AF=0.0497;SAS_AF=0.0153;AA=.|||;VT=SNP;EX_TARGET;EAS_AN=1008;EAS_AC=3;EUR_AN=1006;EUR_AC=50;AFR_AN=1322;AFR_AC=2;AMR_AN=694;AMR_AC=25;SAS_AN=978;SAS_AC=15";
const string vcfLine3 = "1 69428 rs140739101 T G . PASS BSNP=dbSNP_134;EA_AC=313,6535;AA_AC=14,3808;TAC=327,10343;MAF=4.5707,0.3663,3.0647;GTS=GG,GT,TT;EA_GTC=92,129,3203;AA_GTC=1,12,1898;GTC=93,141,5101;DP=110;GL=OR4F5;CP=1.0;CG=0.9;AA=T;CA=.;EXOME_CHIP=no;GWAS_PUBMED=.;FG=NM_001005484.1:missense;HGVS_CDNA_VAR=NM_001005484.1:c.338T>G;HGVS_PROTEIN_VAR=NM_001005484.1:p.(F113C);CDS_SIZES=NM_001005484.1:918;GS=205;PH=probably-damaging:0.999;EA_AGE=.;AA_AGE=.";
var sa = new SupplementaryPositionCreator(new SupplementaryAnnotationPosition(69428));
var dbsnpReader = new DbSnpReader(_renamer);
var dbSnpItem = dbsnpReader.ExtractItem(vcfLine1)[0];
dbSnpItem.SetSupplementaryAnnotations(sa);
var oneKGenItem = _oneKGenReader.ExtractItems(vcfLine2)[0];
oneKGenItem.SetSupplementaryAnnotations(sa);
var evsReader = new EvsReader(_renamer);
var evsItem = evsReader.ExtractItems(vcfLine3)[0];
evsItem.SetSupplementaryAnnotations(sa);
sa.FinalizePositionalAnnotations();
var dbSnp = sa.SaPosition.AlleleSpecificAnnotations["G"].Annotations[DataSourceCommon.GetIndex(DataSourceCommon.DataSource.DbSnp)] as DbSnpAnnotation;
Assert.NotNull(dbSnp);
Assert.Equal(new List <long> {
140739101
}, dbSnp.DbSnp);
Assert.Equal(true, sa.SaPosition.IsRefMinorAllele);
}
public void DeletionAndSnvMerge()
{
// NIR-906
const string vcfLine1 =
"2 193187631 rs774176075 TGTTG T . . RS=774176075;RSPOS=193187632;dbSNPBuildID=144;SSR=0;SAO=0;VP=0x050000000005000002000200;WGT=1;VC=DIV;ASP";
const string vcfLine2 = "2 193187632 rs2592266 G T . . RS=2592266;RSPOS=193187632;dbSNPBuildID=100;SSR=0;SAO=0;VP=0x050000000005150026000100;WGT=1;VC=SNV;ASP;VLD;G5;KGPhase3;CAF=0.01937,0.9806;COMMON=1";
var dbsnpReader = new DbSnpReader(_renamer);
var dbSnpEntry1 = dbsnpReader.ExtractItem(vcfLine1)[0];
var dbSnpEntry2 = dbsnpReader.ExtractItem(vcfLine2)[0];
var sa = new SupplementaryPositionCreator(new SupplementaryAnnotationPosition(193187632));
var additionalEntry = dbSnpEntry1.SetSupplementaryAnnotations(sa);
additionalEntry.SetSupplementaryAnnotations(sa);
var sa2 = new SupplementaryPositionCreator(new SupplementaryAnnotationPosition(193187632));
dbSnpEntry2.SetSupplementaryAnnotations(sa2);
sa.MergeSaCreator(sa2);
sa.FinalizePositionalAnnotations();
Assert.Equal("T", sa.SaPosition.GlobalMajorAllele);
Assert.Equal("0.9806", sa.SaPosition.GlobalMajorAlleleFrequency);
Assert.Equal("G", sa.SaPosition.GlobalMinorAllele);
Assert.Equal("0.01937", sa.SaPosition.GlobalMinorAlleleFrequency);
}
private void CreateDbsnpGaTsv(string fileName)
{
if (fileName == null)
{
return;
}
var benchMark = new Benchmark();
var version = DataSourceVersionReader.GetSourceVersion(fileName);
var dbsnpWriter = new SaTsvWriter(_outputDirectory, version, _genomeAssembly.ToString(),
SaTsvCommon.DbSnpSchemaVersion, InterimSaCommon.DbsnpTag, null, true, new ReferenceSequenceProvider(FileUtilities.GetReadStream(_compressedReferencePath)));
var globalAlleleWriter = new SaTsvWriter(_outputDirectory, version, _genomeAssembly.ToString(),
SaTsvCommon.DbSnpSchemaVersion, InterimSaCommon.GlobalAlleleTag, "GMAF", false, new ReferenceSequenceProvider(FileUtilities.GetReadStream(_compressedReferencePath)));
using (var tsvWriter = new DbsnpGaTsvWriter(dbsnpWriter, globalAlleleWriter))
{
var dbSnpReader = new DbSnpReader(GZipUtilities.GetAppropriateReadStream(fileName), _refNamesDictionary);
TsvWriterUtilities.WriteSortedItems(dbSnpReader.GetDbSnpItems(), tsvWriter);
}
var timeSpan = Benchmark.ToHumanReadable(benchMark.GetElapsedTime());
TsvWriterUtilities.WriteCompleteInfo("DbSNP", version.Version, timeSpan);
}
public void MergeDbSnp1Kg()
{
//NIR-1262
const string vcfLine =
"1 825069 rs4475692 G A,C . . RS=4475692;RSPOS=825069;dbSNPBuildID=111;SSR=0;SAO=0;VP=0x050100000005170126000100;WGT=1;VC=SNV;SLO;ASP;VLD;G5A;G5;GNO;KGPhase3;CAF=0.3227,.,0.6773;COMMON=1";
const string vcfLine1Kg =
"1 825069 rs4475692 G C 100 PASS AC=3392;AF=0.677316;AN=5008;NS=2504;DP=22495;EAS_AF=0.754;AMR_AF=0.5692;AFR_AF=0.6127;EUR_AF=0.7286;SAS_AF=0.7096;AA=g|||;VT=SNP;EAS_AN=1008;EAS_AC=760;EUR_AN=1006;EUR_AC=733;AFR_AN=1322;AFR_AC=810;AMR_AN=694;AMR_AC=395;SAS_AN=978;SAS_AC=694\tGT";
var dbsnpReader = new DbSnpReader(_renamer);
var sa = new SupplementaryPositionCreator(new SupplementaryAnnotationPosition(825069));
foreach (var dbSnpEntry in dbsnpReader.ExtractItem(vcfLine))
{
dbSnpEntry.SetSupplementaryAnnotations(sa);
}
var sa1 = new SupplementaryPositionCreator(new SupplementaryAnnotationPosition(825069));
var onekgReader = new OneKGenReader(_renamer);
foreach (var onekgItem in onekgReader.ExtractItems(vcfLine1Kg))
{
onekgItem.SetSupplementaryAnnotations(sa1);
}
sa.MergeSaCreator(sa1);
sa.FinalizePositionalAnnotations();
Assert.Equal("C", sa.SaPosition.GlobalMajorAllele);
Assert.Equal("G", sa.SaPosition.GlobalMinorAllele);
}
public void MergeSnvAndDeletion()
{
// NIR-906
const string vcfLine1 =
"1 862389 rs6693546 A G . . RS=6693546;RSPOS=862389;dbSNPBuildID=116;SSR=0;SAO=0;VP=0x05010008000515013e000100;WGT=1;VC=SNV;SLO;INT;ASP;VLD;G5;GNO;KGPhase1;KGPhase3;CAF=0.3171,0.6829;COMMON=1";
const string vcfLine2 = "1 862388 rs534606253 GA G . . RS=534606253;RSPOS=862389;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000080005040024000200;WGT=1;VC=DIV;INT;ASP;VLD;KGPhase3;CAF=0.996,0.003994;COMMON=1";
var dbsnpReader = new DbSnpReader(_renamer);
var dbSnpEntry1 = dbsnpReader.ExtractItem(vcfLine1)[0];
var dbSnpEntry2 = dbsnpReader.ExtractItem(vcfLine2)[0];
var sa = new SupplementaryPositionCreator(new SupplementaryAnnotationPosition(862389));
dbSnpEntry1.SetSupplementaryAnnotations(sa);
var sa2 = new SupplementaryPositionCreator(new SupplementaryAnnotationPosition(862389));
var additionalEntry = dbSnpEntry2.SetSupplementaryAnnotations(sa2);
additionalEntry.SetSupplementaryAnnotations(sa2);
sa.MergeSaCreator(sa2);
sa.FinalizePositionalAnnotations();
Assert.Equal("G", sa.SaPosition.GlobalMajorAllele);
Assert.Equal("0.6829", sa.SaPosition.GlobalMajorAlleleFrequency);
Assert.Equal("A", sa.SaPosition.GlobalMinorAllele);
Assert.Equal("0.3171", sa.SaPosition.GlobalMinorAlleleFrequency);
}
public void MultipleDbsnpMerge()
{
// NIR-778, 805. The second dbSNP id is missing from the SA database.
const string vcfLine1 =
"17 3616153 rs34081014 C G . . RS=34081014;RSPOS=3616153;dbSNPBuildID=126;SSR=0;SAO=0;VP=0x050000000005140136000100;WGT=1;VC=SNV;ASP;VLD;GNO;KGPhase1;KGPhase3;CAF=0.9297,0.07029;COMMON=1";
const string vcfLine2 =
"17 3616152 rs71362546 GCTG GCTT,GGTG . . RS=71362546;RSPOS=3616153;dbSNPBuildID=130;SSR=0;SAO=0;VP=0x050100000005000102000810;WGT=1;VC=MNV;SLO;ASP;GNO;NOC";
var sa1 = new SupplementaryPositionCreator(new SupplementaryAnnotationPosition(3616153));
var sa2 = new SupplementaryPositionCreator(new SupplementaryAnnotationPosition(3616153));
var dbsnpReader = new DbSnpReader(_renamer);
var dbSnpItem1 = dbsnpReader.ExtractItem(vcfLine1)[0];
var dbSnpItems = dbsnpReader.ExtractItem(vcfLine2);
dbSnpItem1.SetSupplementaryAnnotations(sa1);
var additionalItems = dbSnpItems.Select(dbSnpItem => dbSnpItem.SetSupplementaryAnnotations(sa1)).ToList();
foreach (var item in additionalItems)
{
item.SetSupplementaryAnnotations(sa2);
}
sa1.MergeSaCreator(sa2);
var dbSnp =
sa1.SaPosition.AlleleSpecificAnnotations["G"].Annotations[DataSourceCommon.GetIndex(DataSourceCommon.DataSource.DbSnp)] as
DbSnpAnnotation;
Assert.NotNull(dbSnp);
Assert.Equal(dbSnp.DbSnp, new List <long> {
34081014, 71362546
});
}
public void MergeDbSnpClinVar()
{
const string vcfLine = "1 225592188 rs387906416 TAGAAGA CTTCTAG . . RS=387906416;RSPOS=225592188;RV;dbSNPBuildID=137;SSR=0;SAO=1;VP=0x050060000605000002110800;GENEINFO=LBR:3930;WGT=1;VC=MNV;PM;NSN;REF;ASP;LSD;OM";
var dbsnpReader = new DbSnpReader(_renamer);
var dbSnpItems = dbsnpReader.ExtractItem(vcfLine);
var sa = new SupplementaryPositionCreator(new SupplementaryAnnotationPosition(225592188));
foreach (var dbSnpItem in dbSnpItems)
{
dbSnpItem.SetSupplementaryAnnotations(sa);
}
var xmlReader = new ClinVarXmlReader(new FileInfo(Resources.TopPath("RCV000087262.xml")), _reader, _sequence);
foreach (var clinVarItem in xmlReader)
{
var sa1 = new SupplementaryPositionCreator(new SupplementaryAnnotationPosition(225592188));
clinVarItem.SetSupplementaryAnnotations(sa1);
sa.MergeSaCreator(sa1);
}
Assert.Equal(1, sa.SaPosition.ClinVarItems.Count);
foreach (var clinVarEntry in sa.SaPosition.ClinVarItems)
{
Assert.Equal(clinVarEntry.ID, "RCV000087262.3");
Assert.Equal(clinVarEntry.MedGenIDs.First(), "C0030779");
Assert.Equal(clinVarEntry.Phenotypes.First(), "Pelger-Huët anomaly");
}
}
public void DuplicateDbsnp()
{
// NIR-853: can't reproduce the problem at dbSnp parsing and merging.
const string vcfLine1 =
"1 8121167 rs34500567 C CAAT,CAATAATAAAATAATAATAATAAT,CAATAAT,CAAT . . RS=34500567;RSPOS=8121167;dbSNPBuildID=126;SSR=0;SAO=0;VP=0x050000000005000002000200;WGT=1;VC=DIV;ASP;CAF=0.9726,.,.,.,.,0.9726;COMMON=1";
const string vcfLine2 =
"1 8121167 rs566669620 C CAATAATAAAAT . . RS=566669620;RSPOS=8121175;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005040024000200;WGT=1;VC=DIV;ASP;VLD;KGPhase3;CAF=0.9726,0.0007987;COMMON=1";
const string vcfLine3 =
"1 8121167 rs59792241 C CAAT,CAATAATAAAATAATAATAATAAT,CAATAAT,CAAT . . RS=59792241;RSPOS=8121205;dbSNPBuildID=137;SSR=0;SAO=0;VP=0x050000000005000002000200;WGT=1;VC=DIV;ASP;CAF=0.9726,.,.,.,.,0.9726;COMMON=1";
var dbsnpReader = new DbSnpReader(_renamer);
var dbSnpItems1 = dbsnpReader.ExtractItem(vcfLine1);
var dbSnpItems2 = dbsnpReader.ExtractItem(vcfLine2);
var dbSnpItems3 = dbsnpReader.ExtractItem(vcfLine3);
var sa1 = new SupplementaryPositionCreator(new SupplementaryAnnotationPosition(8121168));
var sa2 = new SupplementaryPositionCreator(new SupplementaryAnnotationPosition(8121168));
var sa3 = new SupplementaryPositionCreator(new SupplementaryAnnotationPosition(8121168));
var additionalItems = dbSnpItems1.Select(dbSnpItem => dbSnpItem.SetSupplementaryAnnotations(sa1)).ToList();
foreach (var item in additionalItems)
{
item.SetSupplementaryAnnotations(sa1);
}
additionalItems.Clear();
additionalItems.AddRange(dbSnpItems2.Select(dbSnpItem => dbSnpItem.SetSupplementaryAnnotations(sa2)));
foreach (var item in additionalItems)
{
item.SetSupplementaryAnnotations(sa2);
}
additionalItems.Clear();
foreach (var dbSnpItem in dbSnpItems3)
{
additionalItems.Add(dbSnpItem.SetSupplementaryAnnotations(sa3));
}
foreach (var item in additionalItems)
{
item.SetSupplementaryAnnotations(sa3);
}
sa1.MergeSaCreator(sa2);
sa1.MergeSaCreator(sa3);
var dbSnp =
sa1.SaPosition.AlleleSpecificAnnotations["iAAT"].Annotations[DataSourceCommon.GetIndex(DataSourceCommon.DataSource.DbSnp)] as
DbSnpAnnotation;
Assert.NotNull(dbSnp);
Assert.Equal(2, dbSnp.DbSnp.Count);
Assert.Equal(34500567, dbSnp.DbSnp[0]);
Assert.Equal(59792241, dbSnp.DbSnp[1]);
}
public void NoMinorAllele()
{
const string vcfLine = "17 828 rs62053745 T C . . RS=62053745;RSPOS=828;dbSNPBuildID=129;SSR=0;SAO=0;VP=0x050100080005140136000100;WGT=1;VC=SNV;SLO;INT;ASP;VLD;GNO;KGPhase1;KGPhase3;CAF=.,0.7424;COMMON=1";
var sequenceProvider = ParserTestUtils.GetSequenceProvider(828, "T", 'G', ChromosomeUtilities.RefNameToChromosome);
var dbsnpReader = new DbSnpReader(null, sequenceProvider);
var dbSnpEntry = dbsnpReader.ExtractItem(vcfLine).First();
Assert.Equal("C", dbSnpEntry.AltAllele);
}
public void DisregardZeroFreq()
{
const string vcfLine = "1 241369 rs11490246 C T . . RS=11490246;RSPOS=241369;dbSNPBuildID=120;SSR=0;SAO=0;VP=0x050100000005000126000100;WGT=1;VC=SNV;SLO;ASP;GNO;KGPhase3;CAF=0,1;COMMON=0";
var sequenceProvider = ParserTestUtils.GetSequenceProvider(241369, "C", 'G', ChromosomeUtilities.RefNameToChromosome);
var dbsnpReader = new DbSnpReader(null, sequenceProvider);
var dbSnpEntry = dbsnpReader.ExtractItem(vcfLine).First();
Assert.Equal("T", dbSnpEntry.AltAllele);
}
public void RwDbsnpGlobalAlleles()
{
//NIR-1262
var randomPath = Path.Combine(Path.GetTempPath(), Path.GetRandomFileName());
// create our expected data source versions
var dbSnpVersion = new DataSourceVersion("dbSNP", "147", DateTime.Parse("2016-07-26").Ticks);
var expectedDataSourceVersions = new List <DataSourceVersion> {
dbSnpVersion
};
const string vcfLine1 =
"2 141724543 rs112783784 A C,T . . RS=112783784;RSPOS=141724543;dbSNPBuildID=132;SSR=0;SAO=0;VP=0x050100080015140136000100;WGT=1;VC=SNV;SLO;INT;OTH;ASP;VLD;GNO;KGPhase1;KGPhase3;CAF=0.04113,0.9105,0.04832;COMMON=1";
const string vcfLine2 =
"2 141724543 rs4300776 A C . . RS=4300776;RSPOS=141724543;dbSNPBuildID=111;SSR=0;SAO=0;VP=0x050100080015000102000100;WGT=1;VC=SNV;SLO;INT;OTH;ASP;GNO;CAF=0.04113,0.9105;COMMON=1";
var sa = new SupplementaryAnnotationPosition(141724543);
var saCreator = new SupplementaryPositionCreator(sa);
var dbsnpReader = new DbSnpReader(_renamer);
foreach (var dbSnpItem in dbsnpReader.ExtractItem(vcfLine1))
{
dbSnpItem.SetSupplementaryAnnotations(saCreator);
}
foreach (var dbSnpItem in dbsnpReader.ExtractItem(vcfLine2))
{
dbSnpItem.SetSupplementaryAnnotations(saCreator);
}
// write the supplementary annotation file
using (var writer = new SupplementaryAnnotationWriter(randomPath, "chr1", expectedDataSourceVersions))
{
saCreator.FinalizePositionalAnnotations();
writer.Write(saCreator, sa.ReferencePosition);
}
using (var reader = new SupplementaryAnnotationReader(randomPath))
{
// extract the three annotations
var observedAnnotation = reader.GetAnnotation(141724543) as SupplementaryAnnotationPosition;
Assert.NotNull(observedAnnotation);
Assert.Equal("C", observedAnnotation.GlobalMajorAllele);
Assert.Equal("0.9105", observedAnnotation.GlobalMajorAlleleFrequency);
Assert.Equal("T", observedAnnotation.GlobalMinorAllele);
Assert.Equal("0.04832", observedAnnotation.GlobalMinorAlleleFrequency);
}
File.Delete(randomPath);
File.Delete(randomPath + ".idx");
}
public void MissingEntry2()
{
const string vcfLine =
"17 828 rs62053745 T C . . RS=62053745;RSPOS=828;dbSNPBuildID=129;SSR=0;SAO=0;VP=0x050100080005140136000100;WGT=1;VC=SNV;SLO;INT;ASP;VLD;GNO;KGPhase1;KGPhase3;CAF=0.2576,0.7424;COMMON=1";
var dbsnpReader = new DbSnpReader(null, _refChromDict);
var dbSnpEntry = dbsnpReader.ExtractItem(vcfLine)[0];
Assert.Equal(62053745, dbSnpEntry.RsId);
}
public void MissingEntry()
{
const string vcfLine =
"1 241369 rs11490246 C T . . RS=11490246;RSPOS=241369;dbSNPBuildID=120;SSR=0;SAO=0;VP=0x050000000005000126000100;WGT=1;VC=SNV;ASP;GNO;KGPhase3;CAF=0,1;COMMON=0";
var sequenceProvider = ParserTestUtils.GetSequenceProvider(241369, "C", 'A', _refChromDict);
var dbsnpReader = new DbSnpReader(null, sequenceProvider);
var dbSnpEntry = dbsnpReader.ExtractItem(vcfLine).First();
Assert.Equal(11490246, dbSnpEntry.RsId);
}
public void DisregardZeroFreq()
{
const string vcfLine =
"1 241369 rs11490246 C T . . RS=11490246;RSPOS=241369;dbSNPBuildID=120;SSR=0;SAO=0;VP=0x050100000005000126000100;WGT=1;VC=SNV;SLO;ASP;GNO;KGPhase3;CAF=0,1;COMMON=0";
var dbsnpReader = new DbSnpReader(null, _refChromDict);
var dbSnpEntry = dbsnpReader.ExtractItem(vcfLine)[0];
Assert.Equal("T", dbSnpEntry.AlternateAllele);
Assert.Equal(1, dbSnpEntry.AltAlleleFreq);
Assert.Equal(double.MinValue, dbSnpEntry.RefAlleleFreq);
}
public void MissingEntry()
{
const string vcfLine =
"1 241369 rs11490246 C T . . RS=11490246;RSPOS=241369;dbSNPBuildID=120;SSR=0;SAO=0;VP=0x050000000005000126000100;WGT=1;VC=SNV;ASP;GNO;KGPhase3;CAF=0,1;COMMON=0";
var dbsnpReader = new DbSnpReader(null, _refChromDict);
var dbSnpEntry = dbsnpReader.ExtractItem(vcfLine)[0];
Assert.Equal(11490246, dbSnpEntry.RsId);
Assert.Equal(1, dbSnpEntry.AltAlleleFreq);
}
public void NoMinorAllele()
{
const string vcfLine =
"17 828 rs62053745 T C . . RS=62053745;RSPOS=828;dbSNPBuildID=129;SSR=0;SAO=0;VP=0x050100080005140136000100;WGT=1;VC=SNV;SLO;INT;ASP;VLD;GNO;KGPhase1;KGPhase3;CAF=.,0.7424;COMMON=1";
var dbsnpReader = new DbSnpReader(null, _refChromDict);
var dbSnpEntry = dbsnpReader.ExtractItem(vcfLine)[0];
Assert.Equal("C", dbSnpEntry.AlternateAllele);
Assert.Equal(0.7424, dbSnpEntry.AltAlleleFreq);
Assert.Equal(double.MinValue, dbSnpEntry.RefAlleleFreq);
}
public void MergeDbSnpCosmic1Kg()
{
const string vcfLine1 = "1 10228 rs143255646 TA T . . RS=143255646;RSPOS=10229;dbSNPBuildID=134;SSR=0;SAO=0;VP=0x050000020005000002000200;WGT=1;VC=DIV;R5;ASP";
const string vcfLine2 = "1 10228 . TA T 100 PASS AC=2130;AF=0.425319;AN=5008;NS=2504;DP=103152;EAS_AF=0.3363;AMR_AF=0.3602;AFR_AF=0.4909;EUR_AF=0.4056;SAS_AF=0.4949;AA=|||unknown(NO_COVERAGE)";
var sa = new SupplementaryPositionCreator(new SupplementaryAnnotationPosition(10229));
var dbsnpReader = new DbSnpReader(_renamer);
var dbSnpItem1 = dbsnpReader.ExtractItem(vcfLine1)[0];
var additionalItems = new List <SupplementaryDataItem>
{
dbSnpItem1.SetSupplementaryAnnotations(sa)
};
var cosmicItem1 = new CosmicItem("1", 10229, "COSM1000", "TA", "T", "TP53",
new HashSet <CosmicItem.CosmicStudy> {
new CosmicItem.CosmicStudy(null, "carcinoma", "oesophagus")
}, null);
additionalItems.Add(cosmicItem1.SetSupplementaryAnnotations(sa));
var oneKGenItem = _oneKGenReader.ExtractItems(vcfLine2)[0];
additionalItems.Add(oneKGenItem.SetSupplementaryAnnotations(sa));
//sa.Clear();
foreach (var item in additionalItems)
{
item.SetSupplementaryAnnotations(sa);
}
var asa = sa.SaPosition.AlleleSpecificAnnotations["1"];
var dbSnp = asa.Annotations[DataSourceCommon.GetIndex(DataSourceCommon.DataSource.DbSnp)] as DbSnpAnnotation;
var oneKg = asa.Annotations[DataSourceCommon.GetIndex(DataSourceCommon.DataSource.OneKg)] as OneKGenAnnotation;
Assert.NotNull(oneKg);
var oneKgAc = oneKg.OneKgAllAc;
var oneKgAn = oneKg.OneKgAllAn;
Assert.NotNull(oneKgAc);
Assert.NotNull(oneKgAn);
Assert.NotNull(dbSnp);
Assert.NotNull(oneKg);
Assert.Equal(dbSnp.DbSnp, new List <long> {
143255646
});
Assert.Equal("0.425319", (oneKgAc.Value / (double)oneKgAn.Value).ToString(JsonCommon.FrequencyRoundingFormat));
Assert.True(sa.SaPosition.ContainsCosmicId("COSM1000"));
}
public void GetItems_test()
{
var sequence = new SimpleSequence(new string('A', VariantUtils.MaxUpstreamLength) + "T" + new string('G', 10329 - 10285) + "AC", 10284 - VariantUtils.MaxUpstreamLength);
var sequenceProvider = new SimpleSequenceProvider(GenomeAssembly.GRCh37, sequence, ChromosomeUtilities.RefNameToChromosome);
var reader = new DbSnpReader(GetStream(), sequenceProvider);
var items = reader.GetItems().ToList();
Assert.Equal(3, items.Count);
Assert.Equal("\"rs866375379\"", items[0].GetJsonString());
}
public void MissingDbsnpId()
{
const string vcfLine =
"X 21505833 rs12395602 G A,C,T . . RS=12395602;RSPOS=21505833;dbSNPBuildID=120;SSR=0;SAO=0;VP=0x05010008000505051f000101;WGT=1;VC=SNV;SLO;INT;ASP;VLD;G5;HD;GNO;KGPhase1";
var dbsnpReader = new DbSnpReader(null, _refChromDict);
var dbSnpEntries = dbsnpReader.ExtractItem(vcfLine);
Assert.Equal(3, dbSnpEntries.Count);
Assert.Equal("A", dbSnpEntries[0].AlternateAllele);
Assert.Equal(12395602, dbSnpEntries[0].RsId);
Assert.Equal("C", dbSnpEntries[1].AlternateAllele);
Assert.Equal(12395602, dbSnpEntries[1].RsId);
Assert.Equal("T", dbSnpEntries[2].AlternateAllele);
Assert.Equal(12395602, dbSnpEntries[2].RsId);
}
private static ExitCodes ProgramExecution()
{
var referenceProvider = new ReferenceSequenceProvider(FileUtilities.GetReadStream(_compressedReference));
var version = DataSourceVersionReader.GetSourceVersion(_inputFile + ".version");
string outFileName = $"{version.Name}_{version.Version}";
using (var dbSnpReader = new DbSnpReader(GZipUtilities.GetAppropriateReadStream(_inputFile), referenceProvider))
using (var nsaStream = FileUtilities.GetCreateStream(Path.Combine(_outputDirectory, outFileName + SaCommon.SaFileSuffix)))
using (var indexStream = FileUtilities.GetCreateStream(Path.Combine(_outputDirectory, outFileName + SaCommon.SaFileSuffix + SaCommon.IndexSufix)))
using (var nsaWriter = new NsaWriter(nsaStream, indexStream, version, referenceProvider, SaCommon.DbsnpTag, true, true, SaCommon.SchemaVersion, false))
{
nsaWriter.Write(dbSnpReader.GetItems());
}
return(ExitCodes.Success);
}
public void MissingDbsnpId()
{
const string vcfLine =
"X 21505833 rs12395602 G A,C,T . . RS=12395602;RSPOS=21505833;dbSNPBuildID=120;SSR=0;SAO=0;VP=0x05010008000505051f000101;WGT=1;VC=SNV;SLO;INT;ASP;VLD;G5;HD;GNO;KGPhase1";
var sequenceProvider = ParserTestUtils.GetSequenceProvider(21505833, "G", 'G', ChromosomeUtilities.RefNameToChromosome);
var dbsnpReader = new DbSnpReader(null, sequenceProvider);
var dbSnpEntries = dbsnpReader.ExtractItem(vcfLine).ToList();
Assert.Equal(3, dbSnpEntries.Count);
Assert.Equal("A", dbSnpEntries[0].AltAllele);
Assert.Equal(12395602, dbSnpEntries[0].RsId);
Assert.Equal("C", dbSnpEntries[1].AltAllele);
Assert.Equal(12395602, dbSnpEntries[1].RsId);
Assert.Equal("T", dbSnpEntries[2].AltAllele);
Assert.Equal(12395602, dbSnpEntries[2].RsId);
}
public void RefGlobalMajor()
{
// NIR-942
const string vcfLine =
"1 1242707 rs2274262 A G,T . . RS=2274262;RSPOS=1242707;RV;dbSNPBuildID=100;SSR=0;SAO=0;VP=0x0501004a000507013e000100;WGT=1;VC=SNV;SLO;U5;INT;R5;ASP;VLD;G5A;G5;GNO;KGPhase1;KGPhase3;CAF=0.4,0.4,0.2;COMMON=1";
var dbsnpReader = new DbSnpReader(_renamer);
var dbSnpEntry = dbsnpReader.ExtractItem(vcfLine)[0];
var sa = new SupplementaryAnnotationPosition(1242707);
var saCreator = new SupplementaryPositionCreator(sa);
dbSnpEntry.SetSupplementaryAnnotations(saCreator);
saCreator.FinalizePositionalAnnotations();
Assert.Equal("A", sa.GlobalMajorAllele);
Assert.Equal("G", sa.GlobalMinorAllele);
}
public void DisregardZeroFreq()
{
const string vcfLine =
"1 241369 rs11490246 C T . . RS=11490246;RSPOS=241369;dbSNPBuildID=120;SSR=0;SAO=0;VP=0x050100000005000126000100;WGT=1;VC=SNV;SLO;ASP;GNO;KGPhase3;CAF=0,1;COMMON=0";
var dbsnpReader = new DbSnpReader(_renamer);
var dbSnpEntry = dbsnpReader.ExtractItem(vcfLine)[0];
var sa = new SupplementaryAnnotationPosition(828);
var saCreator = new SupplementaryPositionCreator(sa);
dbSnpEntry.SetSupplementaryAnnotations(saCreator);
saCreator.FinalizePositionalAnnotations();
Assert.Equal("T", sa.GlobalMajorAllele);
Assert.Equal("1", sa.GlobalMajorAlleleFrequency);
Assert.Null(sa.GlobalMinorAllele);
Assert.Null(sa.GlobalMinorAlleleFrequency);
}
public void MergeMultipleDbSnpItems()
{
const string vcfLine1 =
"1 1469597 rs3118506 GCG GC,GG . . RS=3118506;RSPOS=1469598;RV;dbSNPBuildID=103;SSR=0;SAO=0;VP=0x050000800005000002000110;WGT=1;VC=SNV;U3;ASP;NOC";
const string vcfLine2 =
"1 1469598 rs368645009 CG C . . RS=368645009;RSPOS=1469599;RV;dbSNPBuildID=138;SSR=0;SAO=0;VP=0x050000800005000002000200;WGT=1;VC=DIV;U3;ASP";
var sa1 = new SupplementaryPositionCreator(new SupplementaryAnnotationPosition(1469599));
var sa2 = new SupplementaryPositionCreator(new SupplementaryAnnotationPosition(1469599));
var dbsnpReader = new DbSnpReader(_renamer);
var dbSnpItems = dbsnpReader.ExtractItem(vcfLine1);
var dbSnpItem2 = dbsnpReader.ExtractItem(vcfLine2)[0];
var additionalItems = dbSnpItems.Select(dbSnpItem => dbSnpItem.SetSupplementaryAnnotations(sa1)).ToList();
foreach (var item in additionalItems)
{
item.SetSupplementaryAnnotations(sa1);
}
additionalItems.Clear();
additionalItems.Add(dbSnpItem2.SetSupplementaryAnnotations(sa2));
foreach (var item in additionalItems)
{
item.SetSupplementaryAnnotations(sa2);
}
sa1.MergeSaCreator(sa2);
var expectedDbSnp = new List <long> {
3118506, 368645009
};
var dbSnp =
sa1.SaPosition.AlleleSpecificAnnotations["1"].Annotations[DataSourceCommon.GetIndex(DataSourceCommon.DataSource.DbSnp)] as
DbSnpAnnotation;
Assert.NotNull(dbSnp);
Assert.Equal(expectedDbSnp, dbSnp.DbSnp);
}
public void MissingDbsnpId()
{
// refactorSA. Annotation for C is missing in the database. have to debug that.
const string vcfLine =
"X 21505833 rs12395602 G A,C,T . . RS=12395602;RSPOS=21505833;dbSNPBuildID=120;SSR=0;SAO=0;VP=0x05010008000505051f000101;WGT=1;VC=SNV;SLO;INT;ASP;VLD;G5;HD;GNO;KGPhase1";
var dbsnpReader = new DbSnpReader(_renamer);
var dbSnpEntries = dbsnpReader.ExtractItem(vcfLine);
var sa = new SupplementaryAnnotationPosition(21505833);
var saCreator = new SupplementaryPositionCreator(sa);
foreach (var dbSnpEntry in dbSnpEntries)
{
dbSnpEntry.SetSupplementaryAnnotations(saCreator);
}
saCreator.FinalizePositionalAnnotations();
var dbSnpA =
sa.AlleleSpecificAnnotations["A"].Annotations[DataSourceCommon.GetIndex(DataSourceCommon.DataSource.DbSnp)] as
DbSnpAnnotation;
Assert.NotNull(dbSnpA);
var dbSnpC =
sa.AlleleSpecificAnnotations["C"].Annotations[DataSourceCommon.GetIndex(DataSourceCommon.DataSource.DbSnp)] as
DbSnpAnnotation;
Assert.NotNull(dbSnpC);
var dbSnpT =
sa.AlleleSpecificAnnotations["T"].Annotations[DataSourceCommon.GetIndex(DataSourceCommon.DataSource.DbSnp)] as
DbSnpAnnotation;
Assert.NotNull(dbSnpT);
Assert.Equal(12395602, dbSnpA.DbSnp[0]);
Assert.Equal(12395602, dbSnpC.DbSnp[0]);
Assert.Equal(12395602, dbSnpT.DbSnp[0]);
}
public void NoMinorAllele1()
{
const string vcfLine =
"17 828 rs62053745 T C . . RS=62053745;RSPOS=828;dbSNPBuildID=129;SSR=0;SAO=0;VP=0x050100080005140136000100;WGT=1;VC=SNV;SLO;INT;ASP;VLD;GNO;KGPhase1;KGPhase3;CAF=0.7424,.;COMMON=1";
var dbsnpReader = new DbSnpReader(_renamer);
var dbSnpEntry = dbsnpReader.ExtractItem(vcfLine)[0];
var sa = new SupplementaryAnnotationPosition(828);
var saCreator = new SupplementaryPositionCreator(sa);
dbSnpEntry.SetSupplementaryAnnotations(saCreator);
saCreator.FinalizePositionalAnnotations();
Assert.Equal("T", sa.GlobalMajorAllele);
Assert.Equal("0.7424", sa.GlobalMajorAlleleFrequency);
Assert.Null(sa.GlobalMinorAllele);
Assert.Null(sa.GlobalMinorAlleleFrequency);
}
public void MergeDbSnpCosmic()
{
const string vcfLine1 = "1 10228 rs143255646 TA T . . RS=143255646;RSPOS=10229;dbSNPBuildID=134;SSR=0;SAO=0;VP=0x050000020005000002000200;WGT=1;VC=DIV;R5;ASP";
var sa = new SupplementaryPositionCreator(new SupplementaryAnnotationPosition(10229));
var dbsnpReader = new DbSnpReader(_renamer);
var dbSnpItem1 = dbsnpReader.ExtractItem(vcfLine1)[0];
var additionalItems = new List <SupplementaryDataItem>
{
dbSnpItem1.SetSupplementaryAnnotations(sa)
};
var cosmicItem1 = new CosmicItem("1", 10229, "COSM1000", "TA", "T", "TP53",
new HashSet <CosmicItem.CosmicStudy> {
new CosmicItem.CosmicStudy(null, "carcinoma", "oesophagus")
}, null);
var cosmicItem2 = new CosmicItem("1", 10229, "COSM1000", "TA", "T", "TP53",
new HashSet <CosmicItem.CosmicStudy> {
new CosmicItem.CosmicStudy("01", "carcinoma", "large_intestine")
}, null);
additionalItems.Add(cosmicItem1.SetSupplementaryAnnotations(sa));
additionalItems.Add(cosmicItem2.SetSupplementaryAnnotations(sa));
//sa.Clear();
foreach (var item in additionalItems)
{
item.SetSupplementaryAnnotations(sa);
}
var dbSnpAnnotation =
sa.SaPosition.AlleleSpecificAnnotations["1"].Annotations[DataSourceCommon.GetIndex(DataSourceCommon.DataSource.DbSnp)] as
DbSnpAnnotation;
Assert.NotNull(dbSnpAnnotation);
Assert.Equal(dbSnpAnnotation.DbSnp, new List <long> {
143255646
});
Assert.True(sa.SaPosition.ContainsCosmicId("COSM1000"));
}
public void MergeDbSnpItems()
{
const string vcfLine1 = "1 10228 rs143255646 TA T . . RS=143255646;RSPOS=10229;dbSNPBuildID=134;SSR=0;SAO=0;VP=0x050000020005000002000200;WGT=1;VC=DIV;R5;ASP";
const string vcfLine2 = "1 10228 rs200462216 TAACCCCTAACCCTAACCCTAAACCCTA T . . RS=200462216;RSPOS=10229;dbSNPBuildID=137;SSR=0;SAO=0;VP=0x050000020005000002000200;WGT=1;VC=DIV;R5;ASP";
var sa = new SupplementaryPositionCreator(new SupplementaryAnnotationPosition(10229));
var dbsnpReader = new DbSnpReader(_renamer);
var dbSnpItem1 = dbsnpReader.ExtractItem(vcfLine1)[0];
var dbSnpItem2 = dbsnpReader.ExtractItem(vcfLine2)[0];
var additionalItems = new List <SupplementaryDataItem>
{
dbSnpItem1.SetSupplementaryAnnotations(sa),
dbSnpItem2.SetSupplementaryAnnotations(sa)
};
//sa.Clear();
foreach (var item in additionalItems)
{
item.SetSupplementaryAnnotations(sa);
}
var dbSnp1 =
sa.SaPosition.AlleleSpecificAnnotations["1"].Annotations[DataSourceCommon.GetIndex(DataSourceCommon.DataSource.DbSnp)] as
DbSnpAnnotation;
Assert.NotNull(dbSnp1);
var dbSnp27 =
sa.SaPosition.AlleleSpecificAnnotations["27"].Annotations[DataSourceCommon.GetIndex(DataSourceCommon.DataSource.DbSnp)] as
DbSnpAnnotation;
Assert.NotNull(dbSnp27);
Assert.Equal(dbSnp1.DbSnp, new List <long> {
143255646
});
Assert.Equal(dbSnp27.DbSnp, new List <long> {
200462216
});
}
public void ReadWriteDbSnpCosmic()
{
var randomPath = Path.Combine(Path.GetTempPath(), Path.GetRandomFileName());
// create our expected data source versions
var dbSnpVersion = new DataSourceVersion("dbSNP", "142", DateTime.Parse("2015-01-02").Ticks);
var cosmicVersion = new DataSourceVersion("COSMIC", "GRCh37_v71", DateTime.Parse("2014-10-21").Ticks);
var expectedDataSourceVersions = new List <DataSourceVersion> {
dbSnpVersion, cosmicVersion
};
// create our expected supplementary annotations
const string vcfLine1 = "1 10228 rs143255646 TA T . . RS=143255646;RSPOS=10229;dbSNPBuildID=134;SSR=0;SAO=0;VP=0x050000020005000002000200;WGT=1;VC=DIV;R5;ASP";
var sa = new SupplementaryAnnotationPosition(10229);
var saCreator = new SupplementaryPositionCreator(sa);
var dbsnpReader = new DbSnpReader(_renamer);
var dbSnpItem1 = dbsnpReader.ExtractItem(vcfLine1)[0];
var additionalItems = new List <SupplementaryDataItem>
{
dbSnpItem1.SetSupplementaryAnnotations(saCreator)
};
var cosmicItem1 = new CosmicItem("1", 10229, "COSM1000", "TA", "T", "TP53",
new HashSet <CosmicItem.CosmicStudy> {
new CosmicItem.CosmicStudy("", "carcinoma", "oesophagus")
}, null);
var cosmicItem2 = new CosmicItem("1", 10229, "COSM1000", "TA", "T", "TP53",
new HashSet <CosmicItem.CosmicStudy> {
new CosmicItem.CosmicStudy("01", "carcinoma", "large_intestine")
}, null);
additionalItems.Add(cosmicItem1.SetSupplementaryAnnotations(saCreator));
additionalItems.Add(cosmicItem2.SetSupplementaryAnnotations(saCreator));
//sa.Clear();
foreach (var item in additionalItems)
{
item.SetSupplementaryAnnotations(saCreator);
}
Assert.Equal(1, sa.CosmicItems.Count);
// the preceeding code has been unit tested in MergeDbSnpCosmic()
// write the supplementary annotation file
using (var writer = new SupplementaryAnnotationWriter(randomPath, "chr1", expectedDataSourceVersions))
{
writer.Write(saCreator, sa.ReferencePosition);
}
// read the supplementary annotation file
using (var reader = new SupplementaryAnnotationReader(randomPath))
{
// extract the three annotations
var observedAnnotation1 = reader.GetAnnotation(10229) as SupplementaryAnnotationPosition;
Assert.NotNull(observedAnnotation1);
var expDbSnp =
sa.AlleleSpecificAnnotations["1"].Annotations[DataSourceCommon.GetIndex(DataSourceCommon.DataSource.DbSnp)] as
DbSnpAnnotation;
Assert.NotNull(expDbSnp);
var obsDbSnp =
observedAnnotation1.AlleleSpecificAnnotations["1"].Annotations[DataSourceCommon.GetIndex(DataSourceCommon.DataSource.DbSnp)] as
DbSnpAnnotation;
Assert.NotNull(obsDbSnp);
Assert.Equal(expDbSnp.DbSnp, obsDbSnp.DbSnp);
Assert.True(observedAnnotation1.ContainsCosmicId(sa.CosmicItems[0].ID));
Assert.Equal(1, observedAnnotation1.CosmicItems.Count);
}
File.Delete(randomPath);
File.Delete(randomPath + ".idx");
}
public void ReadWriteExacDbsnp()
{
var randomPath = Path.Combine(Path.GetTempPath(), Path.GetRandomFileName());
// create our expected data source versions
var dbSnpVersion = new DataSourceVersion("dbSNP", "142", DateTime.Parse("2015-01-02").Ticks);
var cosmicVersion = new DataSourceVersion("COSMIC", "GRCh37_v71", DateTime.Parse("2014-10-21").Ticks);
var expectedDataSourceVersions = new List <DataSourceVersion> {
dbSnpVersion, cosmicVersion
};
// create our expected supplementary annotations
const string vcfLine1 = "2 48010488 rs1042821 G A . . RS=1042821;RSPOS=48010488;RV;dbSNPBuildID=86;SSR=0;SAO=1;VP=0x050168420a05150136100100;GENEINFO=MSH6:2956;WGT=1;VC=SNV;PM;PMC;SLO;NSM;REF;U5;R5;ASP;VLD;G5;GNO;KGPhase1;KGPhase3;LSD;CAF=0.7991,0.2009;COMMON=1";
const string vcfLine2 =
"2 48010488 rs1042821 G A,C 14068898.15 PASS AC=21019,1;AC_AFR=1700,0;AC_AMR=1015,1;AC_Adj=19510,1;AC_EAS=1973,0;AC_FIN=743,0;AC_Het=15722,1,0;AC_Hom=1894,0;AC_NFE=10593,0;AC_OTH=147,0;AC_SAS=3339,0;AF=0.178,8.487e-06;AN=117830;AN_AFR=6388;AN_AMR=9014;AN_Adj=91130;AN_EAS=6792;AN_FIN=5078;AN_NFE=48404;AN_OTH=664;AN_SAS=14790;BaseQRankSum=-4.850e-01;ClippingRankSum=-1.400e-01;DB;DP=1206681;FS=0.000;GQ_MEAN=129.86;GQ_STDDEV=221.88;Het_AFR=1322,0,0;Het_AMR=931,1,0;Het_EAS=1511,0,0;Het_FIN=665,0,0;Het_NFE=8585,0,0;Het_OTH=111,0,0;Het_SAS=2597,0,0;Hom_AFR=189,0;Hom_AMR=42,0;Hom_EAS=231,0;Hom_FIN=39,0;Hom_NFE=1004,0;Hom_OTH=18,0;Hom_SAS=371,0;InbreedingCoeff=0.0376;MQ=60.00;MQ0=0;MQRankSum=0.00;NCC=3737;POSITIVE_TRAIN_SITE;QD=17.46;ReadPosRankSum=0.181;VQSLOD=5.87;culprit=MQ;DP_HIST=3051|9435|11318|5521|9711|11342|4131|1270|615|404|328|266|264|262|196|186|126|115|97|277,133|968|2180|3402|3564|2815|1772|954|551|389|321|263|261|261|196|186|126|115|97|277,0|0|0|1|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0;GQ_HIST=949|2966|347|492|15135|1435|1335|854|421|526|590|416|13672|1951|445|462|255|174|211|16279,24|79|81|124|135|96|110|118|97|180|228|137|182|191|126|171|180|151|192|16229,0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|1";
var sa = new SupplementaryAnnotationPosition(48010488);
var saCreator = new SupplementaryPositionCreator(sa);
var dbsnpReader = new DbSnpReader(_renamer);
var dbSnpItem1 = dbsnpReader.ExtractItem(vcfLine1)[0];
dbSnpItem1.SetSupplementaryAnnotations(saCreator);
var exacReader = new ExacReader(_renamer);
foreach (var exacItem in exacReader.ExtractItems(vcfLine2))
{
exacItem.SetSupplementaryAnnotations(saCreator);
}
// write the supplementary annotation file
using (var writer = new SupplementaryAnnotationWriter(randomPath, "chr2", expectedDataSourceVersions))
{
writer.Write(saCreator, sa.ReferencePosition);
}
// read the supplementary annotation file
using (var reader = new SupplementaryAnnotationReader(randomPath))
{
// extract the three annotations
var observedAnnotation1 = reader.GetAnnotation(48010488) as SupplementaryAnnotationPosition;
Assert.NotNull(observedAnnotation1);
var expDbSnpA =
sa.AlleleSpecificAnnotations["A"].Annotations[DataSourceCommon.GetIndex(DataSourceCommon.DataSource.DbSnp)] as DbSnpAnnotation;
var obsDbSnpA =
observedAnnotation1.AlleleSpecificAnnotations["A"].Annotations[DataSourceCommon.GetIndex(DataSourceCommon.DataSource.DbSnp)] as DbSnpAnnotation;
Assert.NotNull(expDbSnpA);
Assert.NotNull(obsDbSnpA);
// we want to make sure we are reading the values we have written
Assert.Equal(expDbSnpA.DbSnp, obsDbSnpA.DbSnp);
var expExacA =
sa.AlleleSpecificAnnotations["A"].Annotations[DataSourceCommon.GetIndex(DataSourceCommon.DataSource.Exac)] as ExacAnnotation;
var obsExacA =
observedAnnotation1.AlleleSpecificAnnotations["A"].Annotations[DataSourceCommon.GetIndex(DataSourceCommon.DataSource.Exac)] as ExacAnnotation;
Assert.NotNull(expExacA);
Assert.NotNull(obsExacA);
Assert.Equal(expExacA.ExacAllAn, obsExacA.ExacAllAn);
Assert.Equal(expExacA.ExacCoverage, obsExacA.ExacCoverage);
Assert.Equal(Convert.ToDouble(expExacA.ExacAllAc), Convert.ToDouble(obsExacA.ExacAllAc));
Assert.Equal(Convert.ToDouble(expExacA.ExacAfrAc), Convert.ToDouble(obsExacA.ExacAfrAc));
Assert.Equal(Convert.ToDouble(expExacA.ExacAmrAc), Convert.ToDouble(obsExacA.ExacAmrAc));
Assert.Equal(Convert.ToDouble(expExacA.ExacEasAc), Convert.ToDouble(obsExacA.ExacEasAc));
Assert.Equal(Convert.ToDouble(expExacA.ExacFinAc), Convert.ToDouble(obsExacA.ExacFinAc));
Assert.Equal(Convert.ToDouble(expExacA.ExacNfeAc), Convert.ToDouble(obsExacA.ExacNfeAc));
Assert.Equal(Convert.ToDouble(expExacA.ExacOthAc), Convert.ToDouble(obsExacA.ExacOthAc));
Assert.Equal(Convert.ToDouble(expExacA.ExacSasAc), Convert.ToDouble(obsExacA.ExacSasAc));
var expExacC =
sa.AlleleSpecificAnnotations["C"].Annotations[DataSourceCommon.GetIndex(DataSourceCommon.DataSource.Exac)] as ExacAnnotation;
var obsExacC =
observedAnnotation1.AlleleSpecificAnnotations["C"].Annotations[DataSourceCommon.GetIndex(DataSourceCommon.DataSource.Exac)] as ExacAnnotation;
Assert.NotNull(expExacC);
Assert.NotNull(obsExacC);
Assert.Equal(expExacC.ExacCoverage, obsExacC.ExacCoverage);
Assert.Equal(Convert.ToDouble(expExacC.ExacAllAc), Convert.ToDouble(obsExacC.ExacAllAc));
Assert.Equal(Convert.ToDouble(expExacC.ExacAfrAc), Convert.ToDouble(obsExacC.ExacAfrAc));
Assert.Equal(Convert.ToDouble(expExacC.ExacAmrAc), Convert.ToDouble(obsExacC.ExacAmrAc));
Assert.Equal(Convert.ToDouble(expExacC.ExacEasAc), Convert.ToDouble(obsExacC.ExacEasAc));
Assert.Equal(Convert.ToDouble(expExacC.ExacFinAc), Convert.ToDouble(obsExacC.ExacFinAc));
Assert.Equal(Convert.ToDouble(expExacC.ExacNfeAc), Convert.ToDouble(obsExacC.ExacNfeAc));
Assert.Equal(Convert.ToDouble(expExacC.ExacOthAc), Convert.ToDouble(obsExacC.ExacOthAc));
Assert.Equal(Convert.ToDouble(expExacC.ExacSasAc), Convert.ToDouble(obsExacC.ExacSasAc));
}
File.Delete(randomPath);
File.Delete(randomPath + ".idx");
}
